This invention relates generally to computer-aided chemical illustration systems. Specifically, it relates to a system for emulating the illustration tools used in making precise drawings of chemical structures.
The accurate representation of molecules remains a problem for scientists. The use of molecular formulas represents an early attempt at describing molecules. For example, dibromo-ethane can be represented by the molecular formula C.sub.2 H.sub.4 Br.sub.2. However, molecular formulas do not necessarily indicate molecular structure--an aspect which is crucial to the communication of chemical structures.
In particular, molecular formulas do not readily illustrate the variation between isomers, i.e., where two structurally different compounds have the same molecular formula. Even chemical names, which distinguish between isomers, may be difficult to interpret for more complex molecules. For example, carbenicillin, a common antibiotic, has an empirical molecular formula of C.sub.26 H.sub.25 N.sub.2 NaO.sub.6 S. Its chemical name is 1-(5-Indanyl)-N-(2-carboxy-3, 3-dimethyl-7-oxo-4-thia-I-azabicyclo[3.2.0 ] hept-6-yl)-2-phenyl-malonate. However, most readers would not be able to discern carbenicillin's structure from this information. Clearly, a better method is desired to indicate chemical structures.
Structural formulas, first developed by Crum Brown in 1864, attempt to depict three-dimensional molecular structures with two-dimensional drawings. The development and use of structural formulas is well known in the art (see Roberts, J. and Caserio, M., Basic Principles of Organic Chemistry, W. A. Benjamin, Inc., 1977) .
For the most part, structural formulas emphasize ease of drawing over geometric accuracy. Three-dimensional detail is commonly omitted. It is understood that the technical reader will infer the three-dimensional structure from the two-dimensional structural formula.
Methane (CH.sub.4) illustrates this point. It is well established that the carbon atom in methane forms its four single bonds at the corners of a regular tetrahedron, i.e., bond angles equal to 109.5 .degree.. However, it is much easier to draw this as a planar structure. Therefore, methane is represented as a cross-shaped molecule with a carbon (C) atom in the center of four evenly-spaced hydrogen (H) atoms: ##STR1## While methane appears to be a flat molecule with bond angles of 90.degree., the technical reader will infer a tetrahedron. Alternatively, one may draw a more detailed or "projection" structural formula to emphasize methane's tetrahedral nature: ##STR2## Both structural formulas represent two-dimensional depictions of a three-dimensional molecule.
Arguably, a molecule is more accurately represented by three-dimensional models, such as ball and stick or space-filling models. Additional illustration techniques, such as shading or perspective geometry, could be added to structural formulas to yield more accurate renditions. However, these are more difficult and time consuming to create and add little information to the informed scientific reader. The structural formula method is a good compromise between ease of use and geometric accuracy. As a result, it retains great popularity with scientists and technical writers.
While scientists and technical writers have traditionally relied upon templates and pencils to create structural formulas, the human hand can rarely, if ever, achieve the precision that is available with computer-aided systems. As a result, computers have become a powerful tool for the rapid and economical creation of pictures. The use of computer graphics is particularly well suited for automating chemical illustrations.
In computer-aided chemical illustration systems, each object (ring, atom, bond, chemical formula, etc.) exists as an independent constituent with its own attributes. For example, instead of creating a chemical bond by drawing continuously, as one would do by hand, the user need only specify the beginning and ending points. The computer generates a line representing the bond specified by these points. Once an object is entered into the computer, the user may perform various operations which would be difficult or impossible to do manually.
However, current systems have several drawbacks. For example, prior systems have limited bond drawing capabilities. The actual bond drawing method is inefficiently implemented: the user must click a mouse button once at each end of each bond. Also, the user may not change a bond type while drawing. He or she must draw a second bond over the first in order to produce a double bond or enter a different bond mode in which each successive bond will be of the same type.
There are other shortcomings in bond drawing. While one may draw a bond at certain angles (angle constraints) or continuously at any angle, there is no provision for bisecting the angles of existing bonds. For labeling, the user must select a particular atom (usually located at the end of a bond) and type in the label. This cannot be performed "on the fly," e.g., while in a drawing mode with a mouse button depressed. Moreover, there is no provision for the automatic alignment of labels.
Computer-aided systems have automated the process of manipulating or transforming objects. Basic transformation techniques, including move, copy, re-orient, rotate, scale, or flip (mirror), are known in the art. However, current chemical systems have limited transformation facilities. For example, the user is only allowed to pivot (rotate transformation) a structure, such as a ring, around a point while it is being drawn. The user cannot create additional views or "reflections" while in a drawing mode, such as out-of-plane rotations of rings.
In prior systems, the user may draw chemical rings comprised of single and double bonds, for example, the Kekule structure for benzene. However, current implementations cannot recognize a closed chain of bonds as a ring. Without this ability, these systems cannot perform automatic ring operations, such as moving or "shifting" bonds within a ring.
current systems for illustrating chemical structures offer significant advantages over freehand techniques. However, there are notable shortcomings. In particular, these systems fail to recognize or implement many techniques which are needed for the efficient illustration of chemical structures. The present invention provides novel methods and apparatus which fulfills this and other needs.